Auxin signaling plays a vital role in plant growth and development processes like, in apical dominance, tropic responses, lateral root formation, vascular differentiation, embryo patterning and shoot elongation . At the molecular level, most of these processes are controlled by the auxin-response genes [2, 3], and auxin responsiveness is conferred to these genes by conserved promoter elements, including TGA-element (AACGAC), AuxRR-core (core of the auxin response region, GGTCCAT) and AuxRE (auxin response element, TGTCTC). Among these, the AuxRE promoter elements are bound and activated by a plant-specific transcription factors which are called as Auxin Response Factors (ARFs) [4–8]. An ARF protein contains a DNA-binding domain (DBD) in the N-terminal region, a middle region that functions as an activation domain (AD) or repression domain (RD) [9, 10], and a carboxyl-terminal dimerization domain (CTD) that are similar to those found in the C terminus of Aux/IAAs, which is a protein-protein interaction domain that mediates the homo- and hetero- dimerization of ARFs and also the hetero-dimerization of ARF and Aux/IAA proteins [9–14].
It has been reported that, the ARF proteins are encoded by a large gene family, with 23 and 25 members in Arabidopsis and rice, respectively [15, 16]. Expression analysis suggested that these genes are, in general, transcribed in a wide variety of tissues and organs, with an exception of ARF gene cluster on Arabidopsis chromosome 1, which appears to be restricted to embryo genesis/seed development . Classical genetic approaches have led to the identification of ARF gene functions in plant growth and development. For example, arf mutations caused the change in gynoecium patterning (AtARF3) [17–19], impaired hypocotyls response to blue light, growth and auxin sensitivity (AtARF7) [20–24], formation of vascular strands and embryo axis formation (AtARF5) , suppression of hookless phenotype and hypocotyl bending (AtARF2) [26–28], hypocotyl elongation, and auxin homeostasis (AtARF8) [29, 30]. Moreover, the mutants of AtARF sister pairs generally exhibit a much stronger phenotype than that of single mutants, suggesting that closely related AtARFs have somewhat redundant roles in Arabidopsis . In rice, antisense phenotype of OsARF1 gene showed stunted growth, low vigor, curled leaves and sterility, suggesting that the gene is essential for vegetative and reproductive development .
Genetic divergence between Arabidopsis and rice ARF gene family investigated by genome-wide analysis revealed that most of the rice OsARFs are related to Arabidopsis ARFs and fall into sister pairs as in Arabidopsis [16, 32]. The first assembly of maize genome sequence has recently been published , however, to the best of our knowledge, the maize ARF gene family (ZmARF genes) has not been characterized in detail. In this article, we provide detailed information on the genomic structures, chromosomal locations, sequence homology and expression patterns of 31 maize ARF genes. In addition, the phylogenetic relationship between ARF genes in Arabidopsis, rice and maize were also compared, which will help future studies for elucidating the precise roles of ZmARFs in maize growth and development.